8F1J: SigN RNA polymerase early-melted intermediate

SigN RNA polymerase early-melted intermediate bound to mismatch DNA fragment dhsU36mm2 (-12A). Determined by electron microscopy at 2.6 Å resolution. Released 5 Apr 2023.

Method
Electron microscopy
Resolution
2.6 Å
Organisms
Aquifex aeolicus, Escherichia coli
Chains
10
Atoms
30,829
Mol. weight
491.11 kDa
Ligands
ZN, MG
Released
5 Apr 2023

Explore 8F1J in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8F1J contains 185 α-helices and 219 β-strands across 6 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain G: 6 helices, 16 β-strands

ElementResiduesLengthSheet
β-strand12-2091
β-strand23-3191
α-helix35-4915
β-strand52-61102
β-strand7413
α-helix78-869
β-strand90-9234
β-strand97-10592
β-strand108-11143
α-helix112-1143
β-strand11512
α-helix116-1172
β-strand121-12334
β-strand129-13353
β-strand139-150122
β-strand152-15325
α-helix166-1672
β-strand170-17232
β-strand175-17625
β-strand180-189101
β-strand199-20791
α-helix213-23321
Chain H: 11 helices, 17 β-strands
ElementResiduesLengthSheet
β-strand15-1846
β-strand23-3196
α-helix35-4915
β-strand52-61107
β-strand7418
α-helix78-869
β-strand90-9239
β-strand97-10597
β-strand108-11148
α-helix112-1143
α-helix116-1172
β-strand121-12339
β-strand129-13358
β-strand139-150127
β-strand152-153210
β-strand170-17237
β-strand175-176210
β-strand180-190116
β-strand198-207106
α-helix213-22614
α-helix251-2544
β-strand256111
α-helix257-2593
α-helix264-2729
β-strand277111
α-helix278-2825
α-helix286-2905
α-helix297-30812
Chain I: 66 helices, 92 β-strands
ElementResiduesLengthSheet
α-helix5-84
α-helix11-122
β-strand13-14212
α-helix19-202
α-helix29-3911
α-helix49-568
β-strand59-60213
β-strand66-751013
α-helix76-783
α-helix82-887
β-strand93-1041213
β-strand116-1281313
β-strand136-137214
β-strand142-145414
α-helix1461
β-strand147-151515
α-helix1521
β-strand154-160716
β-strand171-177716
β-strand180117
β-strand184-187416
β-strand195-198416
β-strand204-205216
α-helix206-2127
α-helix217-2248
β-strand227-231518
β-strand239-240218
α-helix243-2464
β-strand250119
β-strand255-257320
β-strand260-263420
α-helix2671
β-strand268119
α-helix2691
α-helix271-28010
β-strand284-285218
α-helix289-2924
β-strand296-297218
β-strand301-302221
β-strand309-311321
β-strand315-316218
α-helix319-3268
β-strand332-336518
α-helix347-3537
α-helix360-37011
α-helix378-38912
β-strand396117
α-helix399-40810
α-helix422-43716
β-strand451-454415
α-helix456-47823
α-helix489-4924
α-helix496-50813
β-strand512-514314
α-helix515-5162
α-helix520-5278
β-strand529-531315
α-helix546-5483
α-helix550-5512
α-helix552-5543
β-strand558122
β-strand572-574315
β-strand575122
β-strand576123
β-strand580-581224
β-strand587-595924
β-strand598-6071024
α-helix608-6114
β-strand616-617224
β-strand628124
β-strand634-637424
β-strand642-645424
α-helix647-6493
β-strand652-654324
β-strand662123
α-helix665-6673
α-helix671-6733
α-helix676-68611
β-strand689125
α-helix690-6912
β-strand701112
α-helix705-7117
β-strand716-717226
β-strand722-727627
β-strand731-736627
α-helix738-7403
α-helix741-7422
β-strand748-752527
α-helix753-7542
β-strand757-758228
β-strand763129
β-strand764-765228
β-strand768-769226
β-strand776-777227
β-strand782-785426
β-strand789-790230
β-strand793-794230
β-strand798-804731
β-strand815-819531
α-helix820-8245
β-strand830-8411229
β-strand842132
β-strand847132
β-strand849-850233
α-helix860-8623
β-strand865134
β-strand870135
β-strand871134
α-helix8721
β-strand876-877229
β-strand882-884335
β-strand886-887233
α-helix897-90610
β-strand918-919235
α-helix920-9212
β-strand926-9351029
β-strand936136
α-helix940-9412
α-helix943-97937
α-helix988-9914
α-helix1011-103727
β-strand1040136
β-strand1046-10581329
α-helix1059-10602
β-strand1065-1067331
β-strand1073-1080831
α-helix1082-10843
β-strand1087137
α-helix10921
β-strand1093137
α-helix10941
β-strand1096-1098331
α-helix1102-11065
α-helix1110-113324
α-helix1138-115013
α-helix1161-11633
α-helix1166-117510
β-strand1182-1183212
α-helix1192-120110
β-strand1209-1210238
β-strand1213137
α-helix12191
β-strand1220137
α-helix12211
β-strand1225-1226238
β-strand1227-1234831
β-strand1235125
α-helix1239-12413
β-strand1244-1246339
β-strand1251140
β-strand1252141
β-strand1258140
β-strand1268-1270342
α-helix1272-128110
α-helix1284-12918
α-helix1298-130912
α-helix1321-133111
β-strand1335-1340643
Chain J: 75 helices, 79 β-strands
ElementResiduesLengthSheet
α-helix4-96
β-strand19-24643
α-helix25-262
α-helix27-337
β-strand34-37444
β-strand44145
β-strand51145
α-helix521
α-helix59-624
α-helix78-803
α-helix831
β-strand84146
α-helix851
β-strand91146
α-helix95-995
β-strand102-1121144
α-helix115-1184
α-helix123-1286
α-helix132-1398
β-strand144-148547
β-strand159-160247
α-helix162-17211
β-strand177-179347
α-helix182-1909
α-helix194-20714
α-helix212-22918
α-helix234-2374
β-strand238-244744
α-helix247-2493
α-helix256-2583
α-helix264-28421
α-helix289-30719
β-strand317148
β-strand323148
α-helix324-3252
α-helix327-3315
α-helix3371
α-helix338-3425
β-strand345-347342
β-strand350-354539
β-strand355-357349
β-strand365-369549
α-helix370-3767
α-helix378-38710
α-helix394-40310
α-helix406-41510
β-strand421-424439
α-helix431-4333
β-strand434-437439
β-strand438-442549
β-strand447-449349
α-helix451-4533
α-helix454-4574
β-strand465-469539
α-helix474-4829
β-strand485139
α-helix486-4883
β-strand491150
β-strand498150
α-helix505-5139
β-strand526-527251
α-helix530-5389
β-strand547-5571151
β-strand563-5731151
α-helix574-5807
α-helix589-5913
α-helix598-61114
α-helix615-63521
α-helix641-6433
α-helix645-6473
α-helix650-66920
α-helix675-70127
β-strand703-707552
β-strand713-717552
α-helix721-7277
α-helix734-7418
β-strand745153
β-strand748154
α-helix7531
β-strand754154
α-helix7551
β-strand759153
α-helix766-7672
α-helix769-80335
β-strand809-811355
β-strand820-822356
β-strand825-827357
β-strand830-833457
α-helix836-8394
β-strand843158
β-strand844156
α-helix8471
β-strand848-849259
α-helix8501
β-strand856-858359
β-strand863158
α-helix866-8749
β-strand880-882356
β-strand894-895255
α-helix896-8994
β-strand901160
β-strand908160
α-helix909-9102
α-helix915-92410
α-helix925-9295
β-strand949-951361
β-strand956-961662
β-strand965-967361
β-strand973-975361
β-strand981-985562
β-strand991-996662
α-helix997-9982
β-strand1002-1003261
β-strand1010-1011262
β-strand1016-1019461
β-strand1034-1038563
β-strand1042164
β-strand1046-1048364
β-strand1059-1061364
α-helix1070-10734
β-strand1077-1081563
β-strand1087163
β-strand1089165
α-helix10901
β-strand1096165
β-strand1098-1100363
β-strand1105-1107364
β-strand1122-1123264
α-helix1138-11469
α-helix1148-11503
α-helix1153-11553
β-strand1156166
β-strand1161-1165567
β-strand1170168
β-strand1172168
β-strand1174-1178567
β-strand1187-1189367
β-strand1203-1204267
β-strand1209166
α-helix1214-12163
α-helix1217-12248
α-helix1226-124217
α-helix1250-126011
β-strand1263-1268669
β-strand1279-1281369
α-helix1282-129312
β-strand1301-1305569
α-helix1309-13135
α-helix1319-13257
α-helix1328-133811
β-strand1341-1342243
α-helix1347-13526
α-helix1360-13623
α-helix1363-137210
Chain K: 5 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix7-137
α-helix16-3116
α-helix35-373
α-helix46-5510
α-helix61-7919
Chain M: 22 helices, 15 β-strands
ElementResiduesLengthSheet
α-helix19-246
α-helix30-4112
β-strand47-48270
β-strand115141
α-helix116-1183
α-helix120-12910
α-helix135-14612
β-strand148171
β-strand153172
β-strand154171
α-helix158-1658
α-helix172-18211
β-strand192172
α-helix195-2039
α-helix213-22210
α-helix225-2284
α-helix234-2396
α-helix243-25412
α-helix260-2623
β-strand276-281673
β-strand284-289673
β-strand298-299270
α-helix301-3044
α-helix313-35038
α-helix353-3575
β-strand365174
α-helix367-3737
α-helix378-3847
β-strand390-392373
β-strand395-397373
β-strand403174
β-strand406-407275
β-strand415-416275
α-helix417-42913
α-helix439-4468
α-helix455-46410
α-helix470-4723

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
DNA (36-mer)A, CDNA36Aquifex aeolicus
DNA-directed RNA polymerase subunit alphaG, Hprotein329Escherichia coliP0A7Z4 (AlphaFold model)
DNA-directed RNA polymerase subunit betaIprotein1342Escherichia coliP0A8V2 (AlphaFold model)
DNA-directed RNA polymerase subunit beta'Jprotein1430Escherichia coliP0A8T7 (AlphaFold model)
DNA-directed RNA polymerase subunit omegaKprotein91Escherichia coliP0A800 (AlphaFold model)
RNA polymerase sigma-54 factorMprotein480Escherichia coliP24255
DNA (36-mer)B, DDNA36Aquifex aeolicus
Sequence of entity 1 (A, C), FASTA
>8F1J_1 DNA (36-MER) (chains A, C)
CCAGAAATTGGCACGAAAATTGCCTTAAATACAACG
Sequence of entity 2 (G, H), FASTA
>8F1J_2 DNA-directed RNA polymerase subunit alpha (chains G, H)
MQGSVTEFLKPRLVDIEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVE
IDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITHDGD
VEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPIGRLLVDACYSPV
ERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDVRQP
EVKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSL
TEIKDVLASRGLSLGMRLENWPPASIADE
Sequence of entity 3 (I), FASTA
>8F1J_3 DNA-directed RNA polymerase subunit beta (chains I)
MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQDPEGQYGLEAAFRSVFPIQ
SYSGNSELQYVSYRLGEPVFDVQECQIRGVTYSAPLRVKLRLVIYEREAPEGTVKDIKEQ
EVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNARIIPYR
GSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVIFEIRDNKLQME
LVPERLRGETASFDIEANGKVYVEKGRRITARHIRQLEKDDVKLIEVPVEYIAGKVVAKD
YIDESTGELICAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETLRVDPTNDRL
SALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLLREEIEGSGIL
SKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLS
LGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTR
ERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVT
DEIHYLSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSKGESSLFSRDQVDYMDVSTQQV
VSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAKR
GGVVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPVERG
DVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELACVS
RDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKGETQLTPEEK
LLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEMQLKQAKKDL
SEELQILEAGLFSRIRAVLVAGGVEAEKLDKLPRDRWLELGLTDEEKQNQLEQLAEQYDE
LKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKRRIQPGDKMAGRHGNKGVISKIN
PIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLGMAAKGIGDKINAMLKQQQEVAK
LREFIQRAYDLGADVRQKVDLSTFSDEEVMRLAENLRKGMPIATPVFDGAKEAEIKELLK
LGDLPTSGQIRLYDGRTGEQFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLG
GKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYKNIVDGNHQMEPGMP
ESFNVLLKEIRSLGINIELEDE
Sequence of entity 4 (J), FASTA
>8F1J_4 DNA-directed RNA polymerase subunit beta' (chains J)
MKDLLKFLKAQTKTEEFDAIKIALASPDMIRSWSFGEVKKPETINYRTFKPERDGLFCAR
IFGPVKDYECLCGKYKRLKHRGVICEKCGVEVTQTKVRRERMGHIELASPTAHIWFLKSL
PSRIGLLLDMPLRDIERVLYFESYVVIEGGMTNLERQQILTEEQYLDALEEFGDEFDAKM
GAEAIQALLKSMDLEQECEQLREELNETNSETKRKKLTKRIKLLEAFVQSGNKPEWMILT
VLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQ
EAVDALLDNGRRGRAITGSNKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPY
LRLHQCGLPKKMALELFKPFIYGKLELRGLATTIKAAKKMVEREEAVVWDILDEVIREHP
VLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEA
RALMMSTNNILSPANGEPIIVPSQDVVLGLYYMTRDCVNAKGEGMVLTGPKEAERLYRSG
LASLHARVKVRITEYEKDANGELVAKTSLKDTTVGRAILWMIVPKGLPYSIVNQALGKKA
ISKMLNTCYRILGLKPTVIFADQIMYTGFAYAARSGASVGIDDMVIPEKKHEIISEAEAE
VAEIQEQFQSGLVTAGERYNKVIDIWAAANDRVSKAMMDNLQTETVINRDGQEEKQVSFN
SIYMMADSGARGSAAQIRQLAGMRGLMAKPDGSIIETPITANFREGLNVLQYFISTHGAR
KGLADTALKTANSGYLTRRLVDVAQDLVVTEDDCGTHEGIMMTPVIEGGDVKEPLRDRVL
GRVTAEDVLKPGTADILVPRNTLLHEQWCDLLEENSVDAVKVRSVVSCDTDFGVCAHCYG
RDLARGHIINKGEAIGVIAAQSIGEPGTQLTMRTFHIGGAASRAAAESSIQVKNKGSIKL
SNVKSVVNSSGKLVITSRNTELKLIDEFGRTKESYKVPYGAVLAKGDGEQVAGGETVANW
DPHTMPVITEVSGFVRFTDMIDGQTITRQTDELTGLSSLVVLDSAERTAGGKDLRPALKI
VDAQGNDVLIPGTDMPAQYFLPGKAIVQLEDGVQISSGDTLARIPQESGGTKDITGGLPR
VADLFEARRPKEPAILAEISGIVSFGKETKGKRRLVITPVDGSDPYEEMIPKWRQLNVFE
GERVERGDVISDGPEAPHDILRLRGVHAVTRYIVNEVQDVYRLQGVKINDKHIEVIVRQM
LRKATIVNAGSSDFLEGEQVEYSRVKIANRELEANGKVGATYSRDLLGITKASLATESFI
SAASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGTGYAYHQDRMRRRAAGEAPA
APQVTAEDASASLAELLNAGLGGSDNELELEVLFQGPSSGHHHHHHHHHH
Sequence of entity 5 (K), FASTA
>8F1J_5 DNA-directed RNA polymerase subunit omega (chains K)
MARVTVQDAVEKIGNRFDLVLVAARRARQMQVGGKDPLVPEENDKTTVIALREIEEGLIN
NQILDVRERQEQQEQEAAELQAVTAIAEGRR
Sequence of entity 6 (M), FASTA
>8F1J_6 RNA polymerase sigma-54 factor (chains M)
SEFMKQGLQLRLSQQLAMTPQLQQAIRLLQLSTLELQQELQQALESNPLLEQIDTHEEID
TRETQDSETLDTADALEQKEMPEELPLDASWDTIYTAGTPSGTSGDYIDDELPVYQGETT
QTLQDYLMWQVELTPFSDTDRAIATSIVDAVDETGYLTVPLEDILESIGDEEIDIDEVEA
VLKRIQRFDPVGVAAKDLRDCLLIQLSQFDKTTPWLEEARLIISDHLDLLANHDFRTLMR
VTRLKEDVLKEAVNLIQSLDPRPGQSIQTGEPEYVIPDVLVRKHNGHWTVELNSDSIPRL
QINQHYASMCNNARNDGDSQFIRSNLQDAKWLIKSLESRNDTLLRVSRCIVEQQQAFFEQ
GEEYMKPMVLADIAQAVEMHESTISRVTTQKYLHSPRGIFELKYFFSSHVNTEGGGEASS
TAIRALVKKLIAAENPAKPLSDSKLTSLLSEQGIMVARRTVAKYRESLSIPPSNQRKQLV
Sequence of entity 7 (B, D), FASTA
>8F1J_7 DNA (36-MER) (chains B, D)
CGTTGTATTTATAGCAATTTTCGTGCCAATTTCTGG

Ligands and cofactors

IDNameFormulaCopies
ZNZinc ionZn2
MGMagnesium ionMg1

Primary citation

A general mechanism for transcription bubble nucleation in bacteria. Mueller, A.U., Chen, J., Wu, M. et al. Proc Natl Acad Sci U S A (2023) 120:e2220874120-e2220874120. DOI 10.1073/pnas.2220874120 · PubMed

Other PDB entries of the same protein (UniProt P0A7Z4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

Browse structure collections

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